Molecular characterization of microbial communities in small-scale biodigesters using whole genome shotgun metagenomic approach

Abstract

Increasing attention has been directed towards the role of microbial communities in anaerobic digestion (AD). During AD, microorganisms degrade organic waste, such as animal excrement, through four key phases: hydrolysis, acidogenesis, acetogenesis, and methanogenesis, resulting in digestate and biogas production. Advances in metagenomic techniques, surpassing traditional culture-based methods, have enabled a deeper characterization of the microbial populations involved in this process. However, a knowledge gap remains regarding small-scale biodigesters, particularly those in rural areas. This study employs whole-genome shotgun metagenomics integrating data from metagenomic reads, contigs, and metagenome-assembled genomes (MAGs) can achieve a more comprehensive understanding of microbial taxonomy and functional capabilities in biodigesters. This study investigates the microbial communities in small-scale biodigesters, using taxonomic data from various sources to reveal the functional roles of the microorganisms. The research identified 4 superkingdoms, 115 phyla, 107 classes, 189 orders, 322 families, 738 genera, and 2046 species. Bacteria dominated ranging from 79 to 89%, whereas archaea accounted for 11 to 20% of the community. The eukaryotic microbial’s relative abundance was less than 1%. Both read-based and contig-based classifiers found Proteobacteria, Firmicutes, and Bacteroidetes to be the most abundant bacterial phyla, followed by Actinobacteria and Chloroflexi in cow dung-fed biodigesters. The archaeal community was dominated by Euryarchaeota, with Methanomicrobiales and Methanobacteriales as the predominant orders. Functional analysis reveals that most identified microorganisms contribute indirectly to methanogenesis by playing crucial roles in hydrolysis and acidogenesis through genes involved in the metabolism of organic molecules broken down during the four phases of anaerobic digestion. RAST analysis annotated 11 methanogen-related enzymes and their abundance across different samples. Future research should focus on cultivating and monitoring these identified microbes to determine optimal conditions for maximizing biogas production in laboratory settings, thus advancing environmental bioaugmentation strategies.